jueves, 1 de agosto de 2019

Highlights from infectious disease genomics

Highlights from infectious disease genomics



Highlights from infectious disease genomics

Genome Medicine Collection

New Content ItemNext-generation sequencing approaches are rapidly advancing our understanding of pathogens and clinical management of infectious diseases. This collection showcases recent Genome Medicine articles that have made exciting contributions within this field. Articles in this collection cover insights from whole-genome sequencing into pathogen evolution, transmission, and drug resistance, as well as advances in clinical diagnostics of both viral and bacterial pathogens and treatment strategies. Additionally, it features articles focusing on host immune response and protection against infection, from a genomics perspective.
  1. Content Type:Research

    Residents of long-term care facilities (LTCF) may have high carriage rates of multidrug-resistant pathogens, but are not currently included in surveillance programmes for antimicrobial resistance or healthcare...
    Authors:Hayley J. Brodrick, Kathy E. Raven, Teemu Kallonen, Dorota Jamrozy, Beth Blane, Nicholas M. Brown, Veronique Martin, M. Estée Török, Julian Parkhill and Sharon J. Peacock
    Citation:Genome Medicine 2017 9:70
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  2. Content Type:Research

    Neisseria meningitidis is a globally important cause of meningitis and septicaemia. Twelve capsular groups of meningococci are known, and quadrivalent vaccines against four of these (A...
    Authors:Daniel O’Connor, Elizabeth A. Clutterbuck, Amber J. Thompson, Matthew D. Snape, Maheshi N. Ramasamy, Dominic F. Kelly and Andrew J. Pollard
    Citation:Genome Medicine 2017 9:11
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  3. Content Type:Research

    The emergence of resistance to anti-tuberculosis drugs is a serious and growing threat to public health. Next-generation sequencing is rapidly gaining traction as a diagnostic tool for investigating drug resis...
    Authors:Jody Phelan, Denise M. O’Sullivan, Diana Machado, Jorge Ramos, Alexandra S. Whale, Justin O’Grady, Keertan Dheda, Susana Campino, Ruth McNerney, Miguel Viveiros, Jim F. Huggett and Taane G. Clark
    Citation:Genome Medicine 2016 8:132
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  4. Content Type:Research

    Bloodstream infections remain one of the major challenges in intensive care units, leading to sepsis or even septic shock in many cases. Due to the lack of timely diagnostic approaches with sufficient sensitiv...
    Authors:Silke Grumaz, Philip Stevens, Christian Grumaz, Sebastian O. Decker, Markus A. Weigand, Stefan Hofer, Thorsten Brenner, Arndt von Haeseler and Kai Sohn
    Citation:Genome Medicine 2016 8:73
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  5. Content Type:Research

    A diverse B-cell repertoire is essential for recognition and response to infectious and vaccine antigens. High-throughput sequencing of B-cell receptor (BCR) genes can now be used to study the B-cell repertoir...
    Authors:Jacob D. Galson, Johannes Trück, Elizabeth A. Clutterbuck, Anna Fowler, Vincenzo Cerundolo, Andrew J. Pollard, Gerton Lunter and Dominic F. Kelly
    Citation:Genome Medicine 2016 8:68
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    The Erratum to this article has been published in Genome Medicine 2016 8:81
  7. Content Type:Research

    Recurrent Clostridium difficile infection (CDI) remains problematic, with up to 30 % of individuals diagnosed with primary CDI experiencing at least one episode of recurrence. The success of microbial-based thera...
    Authors:Anna Maria Seekatz, Krishna Rao, Kavitha Santhosh and Vincent Bensan Young
    Citation:Genome Medicine 2016 8:47
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  8. Content Type:Review

    Infections encountered in the cancer setting may arise from intensive cancer treatments or may result from the cancer itself, leading to risk of infections through immune compromise, disruption of anatomic bar...
    Authors:Ying Taur and Eric G. Pamer
    Citation:Genome Medicine 2016 8:40
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  10. Content Type:Research

    Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most common healthcare-associated pathogens. To examine the role of inter-hospital patient sharing on MRSA transmission, a previous study collected...
    Authors:Hsiao-Han Chang, Janina Dordel, Tjibbe Donker, Colin J. Worby, Edward J. Feil, William P. Hanage, Stephen D. Bentley, Susan S. Huang and Marc Lipsitch
    Citation:Genome Medicine 2016 8:18
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  11. Content Type:Research

    Bacterial whole-genome sequencing (WGS) has the potential to identify reservoirs of multidrug-resistant organisms and transmission of these pathogens across healthcare networks. We used WGS to define transmiss...
    Authors:Hayley J. Brodrick, Kathy E. Raven, Ewan M. Harrison, Beth Blane, Sandra Reuter, M. Estée Török, Julian Parkhill and Sharon J. Peacock
    Citation:Genome Medicine 2016 8:4
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  12. Content Type:Research

    Despite the potential to produce antibodies that can neutralize different virus (heterotypic neutralization), there is no knowledge of why vaccination against influenza induces protection predominantly against...
    Authors:Bernardo Cortina-Ceballos, Elizabeth Ernestina Godoy-Lozano, Juan Téllez-Sosa, Marbella Ovilla-Muñoz, Hugo Sámano-Sánchez, Andrés Aguilar-Salgado, Rosa Elena Gómez-Barreto, Humberto Valdovinos-Torres, Irma López-Martínez, Rodrigo Aparicio-Antonio, Mario H. Rodríguez and Jesús Martínez-Barnetche
    Citation:Genome Medicine 2015 7:124
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  13. Content Type:Method

    We report unbiased metagenomic detection of chikungunya virus (CHIKV), Ebola virus (EBOV), and hepatitis C virus (HCV) from four human blood samples by MinION nanopore sequencing coupled to a newly developed, ...
    Authors:Alexander L. Greninger, Samia N. Naccache, Scot Federman, Guixia Yu, Placide Mbala, Vanessa Bres, Doug Stryke, Jerome Bouquet, Sneha Somasekar, Jeffrey M. Linnen, Roger Dodd, Prime Mulembakani, Bradley S. Schneider, Jean-Jacques Muyembe-Tamfum, Susan L. Stramer and Charles Y. Chiu
    Citation:Genome Medicine 2015 7:99
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  14. Content Type:Method

    Mycobacterium tuberculosis drug resistance (DR) challenges effective tuberculosis disease control. Current molecular tests examine limited numbers of mutations, and although whole genome sequenci...
    Authors:Francesc Coll, Ruth McNerney, Mark D Preston, José Afonso Guerra-Assunção, Andrew Warry, Grant Hill-Cawthorne, Kim Mallard, Mridul Nair, Anabela Miranda, Adriana Alves, João Perdigão, Miguel Viveiros, Isabel Portugal, Zahra Hasan, Rumina Hasan, Judith R Glynn…
    Citation:Genome Medicine 2015 7:51
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  15. Content Type:Research

    During intra-erythrocytic development, late asexually replicating Plasmodium falciparum parasites sequester from peripheral circulation. This facilitates chronic infection and is linked to severe disease and orga...
    Authors:Karell G Pelle, Keunyoung Oh, Kathrin Buchholz, Vagheesh Narasimhan, Regina Joice, Danny A Milner, Nicolas MB Brancucci, Siyuan Ma, Till S Voss, Ken Ketman, Karl B Seydel, Terrie E Taylor, Natasha S Barteneva, Curtis Huttenhower and Matthias Marti
    Citation:Genome Medicine 2015 7:19
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  16. Content Type:Review

    The current therapeutic arsenal against viral infections remains limited, with often poor efficacy and incomplete coverage, and appears inadequate to face the emergence of drug resistance. Our understanding of...
    Authors:Benoît de Chassey, Laurène Meyniel-Schicklin, Jacky Vonderscher, Patrice André and Vincent Lotteau
    Citation:Genome Medicine 2014 6:115
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  17. Content Type:Research

    During the latter half of the natural 48-h intraerythrocytic life cycle of human Plasmodium falciparuminfection, parasites sequester deep in endothelium of tissues, away from the spleen and inaccessible to perip...
    Authors:Daria Van Tyne, Yan Tan, Johanna P Daily, Steve Kamiza, Karl Seydel, Terrie Taylor, Jill P Mesirov, Dyann F Wirth and Danny A Milner
    Citation:Genome Medicine 2014 6:110
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  18. Content Type:Research

    Toxigenic Corynebacterium ulcerans can cause a diphtheria-like illness in humans and have been found in domestic animals, which were suspected to serve as reservoirs for a zoonotic transmission. Additionally, tox...
    Authors:Dominik M Meinel, Gabriele Margos, Regina Konrad, Stefan Krebs, Helmut Blum and Andreas Sing
    Citation:Genome Medicine 2014 6:113
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  19. Content Type:Method

    Bacteria have been shown to generate constant genetic variation in a process termed phase variation. We present a tool based on whole genome sequencing that allows detection and quantification of coexisting ge...
    Authors:Amir Goldberg, Ofer Fridman, Irine Ronin and Nathalie Q Balaban
    Citation:Genome Medicine 2014 6:112
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  20. Content Type:Research

    Sepsis, a leading cause of morbidity and mortality, is not a homogeneous disease but rather a syndrome encompassing many heterogeneous pathophysiologies. Patient factors including genetics predispose to poor o...
    Authors:Ephraim L Tsalik, Raymond J Langley, Darrell L Dinwiddie, Neil A Miller, Byunggil Yoo, Jennifer C van Velkinburgh, Laurie D Smith, Isabella Thiffault, Anja K Jaehne, Ashlee M Valente, Ricardo Henao, Xin Yuan, Seth W Glickman, Brandon J Rice, Micah T McClain, Lawrence Carin…
    Citation:Genome Medicine 2014 6:111
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  21. Content Type:Research

    Dendritic cells localize throughout the body, where they can sense and capture invading pathogens to induce protective immunity. Hence, harnessing the biology of tissue-resident dendritic cells is fundamental ...
    Authors:Dorothée Duluc, Romain Banchereau, Julien Gannevat, Luann Thompson-Snipes, Jean-Philippe Blanck, Sandra Zurawski, Gerard Zurawski, Seunghee Hong, Jose Rossello-Urgell, Virginia Pascual, Nicole Baldwin, Jack Stecher, Michael Carley, Muriel Boreham and SangKon Oh
    Citation:Genome Medicine 2014 6:98
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  22. Content Type:Software

    Rapid molecular typing of bacterial pathogens is critical for public health epidemiology, surveillance and infection control, yet routine use of whole genome sequencing (WGS) for these purposes poses significa...
    Authors:Michael Inouye, Harriet Dashnow, Lesley-Ann Raven, Mark B Schultz, Bernard J Pope, Takehiro Tomita, Justin Zobel and Kathryn E Holt
    Citation:Genome Medicine 2014 6:90
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  23. Content Type:Method

    Whole genome sequencing is increasingly used to study phenotypic variation among infectious pathogens and to evaluate their relative transmissibility, virulence, and immunogenicity. To date, relatively little ...
    Authors:Maha R Farhat, B Jesse Shapiro, Samuel K Sheppard, Caroline Colijn and Megan Murray
    Citation:Genome Medicine 2014 6:101
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